GapMind for catabolism of small carbon sources

 

Protein WP_010530627.1 in Lentibacillus jeotgali Grbi

Annotation: NCBI__GCF_000224785.1:WP_010530627.1

Length: 246 amino acids

Source: GCF_000224785.1 in NCBI

Candidate for 18 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
L-rhamnose catabolism LRA1 med NAD(P)+-dependent L-rhamnose 1-dehydrogenase (EC 1.1.1.378; EC 1.1.1.173) (characterized) 43% 98% 184.1 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
L-isoleucine catabolism ivdG lo 3-hydroxyacyl-CoA dehydrogenase IvdG; EC 1.1.1.35 (characterized, see rationale) 35% 98% 156.4 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
L-rhamnose catabolism LRA5 lo 2-dehydro-3-deoxy-L-rhamnonate dehydrogenase (NAD(+)); 2-keto-3-deoxy-L-rhamnonate dehydrogenase; KDRDH; L-KDR dehydrogenase; L-KDR 4-dehydrogenase; EC 1.1.1.401 (characterized) 34% 95% 142.9 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
D-sorbitol (glucitol) catabolism srlD lo Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) (characterized) 36% 96% 135.6 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
D-mannitol catabolism mt2d lo NADP-dependent mannitol dehydrogenase; MtDH; Mannitol 2-dehydrogenase [NADP(+)]; Allergen Alt a 8; EC 1.1.1.138 (characterized) 32% 92% 134.8 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
D-galactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 36% 96% 131.7 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
lactose catabolism galdh lo Probable galactose dehydrogenase GalD; EC 1.1.1.- (characterized) 36% 96% 131.7 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
4-hydroxybenzoate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
4-hydroxybenzoate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
L-arginine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
L-citrulline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
L-lysine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
phenylacetate catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
phenylacetate catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
L-phenylalanine catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
L-phenylalanine catabolism paaH lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
L-proline catabolism fadB lo Peroxisomal multifunctional enzyme A; MFE-A; MFE-1; EC 1.1.1.35 (characterized) 36% 53% 131.3 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9
D-xylose catabolism xdh lo D-xylose 1-dehydrogenase (EC 1.1.1.175) (characterized) 33% 93% 125.6 3-oxoacyl-[acyl-carrier-protein] reductase FabG; 3-ketoacyl-acyl carrier protein reductase; Beta-Ketoacyl-acyl carrier protein reductase; Beta-ketoacyl-ACP reductase; EC 1.1.1.100 71% 335.9

Sequence Analysis Tools

View WP_010530627.1 at NCBI

Find papers: PaperBLAST

Find functional residues: SitesBLAST

Search for conserved domains

Find the best match in UniProt

Compare to protein structures

Predict transmenbrane helices: Phobius

Predict protein localization: PSORTb

Find homologs in fast.genomics

Fitness BLAST: loading...

Sequence

MLDGKSALVTGASRGIGRAIALELARQGANVAVNYSGSEDKAQAVVEEIKQMGVQSFKIQ
ANVADEKEAKAMVKQVVSEFDSLDILVNNAGINRDNLLMRMKEDEFDQVIDTNLKGVFQC
TKAVSRQMMKQKGGRIINVSSIVGVSGNAGQANYTAAKAGVIGLTKSTAKEFASRNILVN
AVAPGFISTDMTDALTEEQKEGMLSVIPLEKLGEPDDVARVVRFLASDDAKYITGQTIHI
DGGMVM

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory